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- PDB-4fwk: Crystal structure of Salmonella typhimurium propionate kinase (Td... -

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Basic information

Entry
Database: PDB / ID: 4fwk
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with AMP
ComponentsPropionate kinase
KeywordsTRANSFERASE / Kinase / Acetate and Sugar Kinases/Hsc70/Actin (ASKHA) superfamily / Propionate kinase / TdcD / AMP / Short-Chain Fatty Acid
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChittori, S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.
Authors: Chittori, S. / Simanshu, D.K. / Banerjee, S. / Murthy, A.M.V. / Mathivanan, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJul 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6563
Polymers45,2461
Non-polymers4092
Water1,24369
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3116
Polymers90,4932
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7690 Å2
ΔGint-42 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.419, 111.419, 66.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein Propionate kinase


Mass: 45246.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: oxd-2, STM3242, tdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 % / Mosaicity: 0.601 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris pH 6.0, 30% hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 13, 2009 / Details: Mirror
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12025 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.118 / Χ2: 0.991 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.950.58511281.737195.9
2.9-3.025.70.52811891.637199.7
3.02-3.156.30.41911761.5981100
3.15-3.326.40.27711941.3621100
3.32-3.536.40.19612151.084199.9
3.53-3.86.40.13711810.8211100
3.8-4.186.50.10112160.6791100
4.18-4.796.40.07312120.4851100
4.79-6.036.40.0812310.531100
6.03-506.10.05412830.357199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E1Y

2e1y


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.393 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 575 4.8 %RANDOM
Rwork0.2312 ---
obs0.2336 12025 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.1 Å2 / Biso mean: 46.9403 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 27 69 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213003
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.9564084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3485393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75823.36125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0115462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0091522
X-RAY DIFFRACTIONr_chiral_restr0.0540.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212270
X-RAY DIFFRACTIONr_mcbond_it0.2331.51946
X-RAY DIFFRACTIONr_mcangle_it0.42423098
X-RAY DIFFRACTIONr_scbond_it0.26931057
X-RAY DIFFRACTIONr_scangle_it0.4944.5986
LS refinement shellResolution: 2.797→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 44 -
Rwork0.347 771 -
all-815 -
obs--93.89 %

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